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Profiling of soma and neurite transcriptomes

ABSTRACT: We report mRNA profiles of subcellularly localized transcriptomes (soma and neurite) of two mouse cell lines, N2A and CAD, as well as primary cortical neurons from E18.5 mice. We also performed this fractionation and sequencing after RNAi knockdown (cell lines) or in knockout mice (primary cortical neurons) of the RNA-binding proteins muscleblind 1 and 2 (Mbnl1 and Mbnl2). Fractionate neurons using porous transwell membranes. Isolate poly-A RNA.

ORGANISM(S): Mus musculus

SUBMITTER: Matthew Taliaferro

PROVIDER: E-GEOD-67828 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Profiling of soma and neurite transcriptomes

Project description:We report mRNA profiles of subcellularly localized transcriptomes (soma and neurite) of two mouse cell lines, N2A and CAD, as well as primary cortical neurons from E18.5 mice. We also performed this fractionation and sequencing after RNAi knockdown (cell lines) or in knockout mice (primary cortical neurons) of the RNA-binding proteins muscleblind 1 and 2 (Mbnl1 and Mbnl2).

2016-02-19 | GSE67828 | GEO

Global proteome of neurite and soma isolated from primary cortical neurons

Project description:Proteome comparison of neurite and soma total protein extracts isolated from mouse cortical neurons.

2022-11-15 | PXD028300 | Pride

Muscleblind-like compound knockout models for myotonic dystrophy

Project description:Myotonic dystrophy (DM) is a multi-systemic disease that severely impacts cardiac and skeletal muscle functions as well as the central nervous system. DM is unusual because it is RNA-mediated disease due to the expression of C(C)UG expansion RNAs that inhibit the activities of the muscleblind-like (MBNL) proteins. In mice, studies using Mbnl1 and Mbnl2 single knockouts have revealed that Mbnl1 plays a predominant role in skeletal and heart muscle alternative splicing regulation while Mbnl2 performs an analogous splicing function in the brain. However, Mbnl single knockout models fail to recapitulate the full-range of adult-onset DM muscle symptoms. Here, we report that Mbnl1; Mbnl2 double knockouts are embryonic lethal while Mbnl1-/-; Mbnl2+/- mice, which express no Mbnl1 and reduced levels of Mbnl2, are viable but develop cardinal features of adult-onset DM cardiac and skeletal muscle disease including reduced lifespan, heart conduction block, severe myotonia and progressive skeletal muscle weakness. Mbnl2 protein levels are elevated in both Mbnl1-/- and Mbnl1-/-; Mbnl2+/- knockouts where Mbnl2 targets Mbnl1-regulated exons. These findings support the MBNL loss-of-function model for DM and provide novel Mbnl compound knockout models to investigate the molecular pathways disrupted by RNA-mediated disease. Mbnl2 protein-RNA interactions were assessed in 4-month-old WT and Mbnl1-/- quadriceps muscles in triplicates by HITS-CLIP.

2013-12-01 | E-GEOD-47794 | biostudies-arrayexpress

Transcriptome-wide Regulation of Splicing and mRNA Localization by Muscleblind Proteins

Project description:The Muscleblind-like (Mbnl) family of RNA-binding proteins plays important roles in muscle and eye development and in Myotonic Dystrophy (DM), where expanded CUG or CCUG repeats functionally deplete Mbnl proteins. We identified transcriptome-wide functional and biophysical targets of Mbnl proteins in brain, heart, muscle, and myoblasts using RNA sequencing and crosslinking/immunoprecipitation-sequencing approaches. This analysis identified several hundred splicing events whose regulation depended on Mbnl function, in a pattern indicative of functional interchangeability between Mbnl1 and Mbnl2. A nucleotide resolution RNA map associated repression or activation of exon splicing with Mbnl binding near either 3' splice site or near the downstream 5' splice site, respectively. Transcriptomic analysis of sub-cellular compartments uncovered a global role for Mbnls in regulating localization of mRNAs encoding membrane, synaptic and other proteins in both mouse and Drosophila cells, and Mbnls also contribute to protein secretion. These findings hold several new implications for DM pathogenesis. To assess global functions of Muscleblind proteins, RNA-Seq was performed using WT and Mbnl1 KO brain, heart, and muscle (5 mice each). Additionally, C2C12 mouse myoblasts were depleted of Mbnl1, Mbnl2, or both. Subcellular fractionation experiments were performed to analyze mRNA localization following depletion of Mbnl1 and Mbnl2 in C2C12 mouse myoblasts, and following depletion of Mbnl in Drosophila S-2R+ cells. CLIP-Seq was also performed against Mbnl1 in mouse brain, heart, muscle, and C2C12 myoblasts. Finally, ribosome footprinting was performed with C2C12 mouse myoblasts that were depleted of Mbnl1, Mbnl2, or both.

2012-08-17 | E-GEOD-39911 | biostudies-arrayexpress

Muscleblind-Like 2 mediated alternative splicing in the developing bain by mRNA sequencing

Project description:We have identified Mbnl2 mediated splicing events and mRNA expression regulation by comparing WT and Mbnl2 ?E2/?E2 mouse hippocampii using Affymetrix Mouse Exon Junction Array and mRNA sequencing. The splicing microarray data has already been submitted under GSE37908 which also includes a re-analysis of RNA-seq data. The TableS1.xls contains Splicing microarray analysis data of Mbnl2+/+ vs. MBNL2 ?E2/?E2 knockout hippocampus. The TableS2.xls files contain RNA-Seq, Gene Ontology, HITS-CLIP and CIMS summary of Mbnl2+/+ vs. MBNL2 ?E2/?E2 knockout hippocampus. The file contents are descibed in the 'TableS1_S2_readme.pdf' and data processing details are included in the 'data_processing_readme.pdf' file. 6 total samples were analyzed: brains from 3 WT and 3 MBNL2 ?E2/?E2 female mice, all 2-3 months of age.

2012-08-16 | E-GEOD-38497 | biostudies-arrayexpress

Modulation of ESRP2 and MBNL2 in normal kidney and clear cell renal cell carcinoma cell lines for analysis of stability programs

Project description:While analyzing mRNA expression profiles of clear cell renal cell carcinoma (ccRCC) tumors, we found that the mRNAs that are bound at their 3' UTRs by muscleblind-like splicing regulator 2 (Mbnl2) and epithelial splicing regulatory protein 2 (ESRP2) are up-regulated in tumor compared to patient-matched normal tissues. Given that MBNL2 increases the stability of its targets and ESRP2 destabilizes its targets, we predicted that, in ccRCC tumors, MBNL2 activity increases, while ESRP2 activity decreases. To investigate the effect of each of these two RNA-binding proteins (RBPs) on the transcriptome of the cell, we used shRNA to knockdown MBNL2 in two different cell line models of ccRCC (786-O and A-498), and also to knockdown ESRP2 in normal primary renal proximal tubule epithelial cells (PRPTEC). RNA-seq revealed that MBNL2 knockdown partially reverses the ccRCC-associated transcriptome in ccRCC cell lines, whereas ESRP2 knockdown shifts the transcriptome of PRPTEC toward that of ccRCC.

2018-03-23 | GSE83999 | GEO

Compound loss of muscleblind-like function in myotonic dystrophy

2013-12-01 | GSE47794 | GEO

Electrical stimulation with a conductive ITO glass promotes neurite outgrowth and its putative mechanisms of action for direct and alternating current in primary cortical neurons

Project description:In this study, we investigated the effects of DCS and ACS on rat primary cortical neurons. Our goal was to probe the optimal stimulation parameters and underlying mechanism of ES on the primary cortical neurons.

2022-06-30 | GSE207117 | GEO

E-MTAB-9045

Project description:Nuclear SLIC-CAGE of human cortical neurons from Cornelia de Lange Syndrome patients and control individuals

2025-01-16 | E-MTAB-9045 | ExpressionAtlas

Mbnl2

Project description:Rattus norvegicus Mbnl2, muscleblind-like splicing regulator 2 [Source:RGD Symbol;Acc:1591755], is differentially expressed in 34 experiment(s);

| ENSRNOG00000010737 | ExpressionAtlas

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